Abstract
BackgroundDevelopment and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs.ResultsThis study presents whole genome analyses of one highly virulent Fo koae isolate and one non-pathogenic F. oxysporum (Fo) isolate. These analyses allowed for the identification of putative lineage-specific DNA and predicted genes necessary for disease development on koa. Using putative chromosomes and predicted gene comparisons, Fo koae-exclusive, virulence genes were identified. The putative lineage-specific DNA included identified genes encoding products secreted in xylem (e. g., SIX1 and SIX6) that may be necessary for disease development on koa. Unique genes from Fo koae were used to develop pathogen-specific PCR primers. These diagnostic primers allowed target amplification in the characterized highly virulent Fo koae isolates but did not allow product amplification in low-virulence or non-pathogenic isolates of Fo. Thus, primers developed in this study will be useful for early detection and monitoring of highly virulent strains of Fo koae. Isolate verification is also important for disease resistance-breeding programs that require a diverse set of highly virulent Fo koae isolates for their disease-screening assays to develop disease-resistant koa.ConclusionsThese results provide the framework for understanding the pathogen genes necessary for koa wilt disease and the genetic variation of Fo koae populations across the Hawaiian Islands.
Highlights
Development and application of Deoxyribonucleic acid (DNA)-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [F. oxysporum (Fo) koae; cause of koa wilt disease on Acacia koa] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs
Libraries resulted in 397,390,528 reads with 1245x coverage for pathogenic isolate f. sp. koae (Fo koae) 44 and 385,805,256 reads with 1150x coverage for non-pathogenic isolate Fo 170
Whole genome phylogenetic analysis A whole-genome maximum likelihood phylogeny was constructed to elucidate the evolutionary relationships of Fo koae 44 and Fo 170 compared with other Fusarium spp. and F. oxysporum formae speciales (Additional File 9)
Summary
Development and application of DNA-based methods to distinguish highly virulent isolates of Fusarium oxysporum f. sp. koae [Fo koae; cause of koa wilt disease on Acacia koa (koa)] will help disease management through early detection, enhanced monitoring, and improved disease resistance-breeding programs. Intraspecific genomic comparisons between pathogenic and non-pathogenic fungal isolates can elucidate key factors required for pathogenicity in plant hosts [1, 2] These factors include unique genes that are vital for the pathogen to cause disease, but can provide tools to differentiate pathogens and non-pathogens for detection and monitoring. Cubense [12, 13], and transposable elements (i.e., miniature impala elements) have been documented to enhance effector diversity [14,15,16] These factors help distinguish pathogenicity and/or virulence in Fusaria and could provide a basis for early detection of pathogens which would facilitate disease management programs through efforts to reduce pathogen spread to uninfested sites
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